So I don't know what to do and today I was going to backup my databases as I have users details etc on them and I thought it would be easy, just export them and done and now I have this error and I need it back online ASAP!

For starters, I would look to the developers of the package you are running.

A method for testing if there is a MySQL problem would be to install something like Wordpress (temporarily) and make sure it runs reliably. If it (wordpress) does run right, 90% chance the app is causing the crash. I would also look at the my.ini/my.cnf recommendations for the package. You could be hitting memory allocation issues, etc.